Thermodynamics and Kinetics of Folding of a Small Peptide

We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at suitable temperatures. The results of these canonical simulations are compared with that of a generalized-ensemble simulation. Our work demonstrates that concepts of folding which were developed in the past for minimalist models hold also for this peptide when simulated with an all-atom force field

Final spins from the merger of precessing binary black holes

The inspiral of binary black holes is governed by gravitational radiation reaction at binary separations r < 1000 M, yet it is too computationally expensive to begin numerical-relativity simulations with initial separations r > 10 M. Fortunately, binary evolution between these separations is well described by post-Newtonian equations of motion. We examine how this post-Newtonian evolution affects the distribution of spin orientations at separations r ~ 10 M where numerical-relativity simulations typically begin. Although isotropic spin distributions at r ~ 1000 M remain isotropic at r ~ 10 M, distributions that are initially partially aligned with the orbital angular momentum can be significantly distorted during the post-Newtonian inspiral. Spin precession tends to align (anti-align) the binary black hole spins with each other if the spin of the more massive black hole is initially partially aligned (anti-aligned) with the orbital angular momentum, thus increasing (decreasing) the average final spin. Spin precession is stronger for comparable-mass binaries, and could produce significant spin alignment before merger for both supermassive and stellar-mass black hole binaries. We also point out that precession induces an intrinsic accuracy limitation (< 0.03 in the dimensionless spin magnitude, < 20 degrees in the direction) in predicting the final spin resulting from the merger of widely separated binaries.Comment: 20 pages, 16 figures, new PN terms, submitted to PR

Virtual Resonant States in Two-Photon Decay Processes: Lower-Order Terms, Subtractions, and Physical Interpretations

We investigate the two-photon decay rate of a highly excited atomic state which can decay to bound states of lower energy via cascade processes. We show that a naive treatment of the process, based on the introduction of phenomenological decay rates for the intermediate, resonant states, leads to lower-order terms which need to be subtracted in order to obtain the coherent two-photon correction to the decay rate. The sum of the lower-order terms is exactly equal to the one-photon decay rate of the initial state, provided the naive two-photon decay rates are summed over all available two-photon channels. A quantum electrodynamics (QED) treatment of the problem leads to an "automatic" subtraction of the lower-order terms.Comment: 8 pages, RevTe

Quantitative trait locus analysis of parasitoid counteradaptation to symbiont-conferred resistance.

Insect hosts and parasitoids are engaged in an intense struggle of antagonistic coevolution. Infection with heritable bacterial endosymbionts can substantially increase the resistance of aphids to parasitoid wasps, which exerts selection on parasitoids to overcome this symbiont-conferred protection (counteradaptation). Experimental evolution in the laboratory has produced counteradapted populations of the parasitoid wasp Lysiphlebus fabarum. These populations can parasitize black bean aphids (Aphis fabae) protected by the bacterial endosymbiont Hamiltonella defensa, which confers high resistance against L. fabarum. We used two experimentally evolved parasitoid populations to study the genetic architecture of the counteradaptation to symbiont-conferred resistance by QTL analysis. With simple crossing experiments, we showed that the counteradaptation is a recessive trait depending on the maternal genotype. Based on these results, we designed a customized crossing scheme to genotype a mapping population phenotyped for the ability to parasitize Hamiltonella-protected aphids. Using 1835 SNP markers obtained by ddRAD sequencing, we constructed a high-density linkage map consisting of six linkage groups (LGs) with an overall length of 828.3 cM and an average marker spacing of 0.45 cM. We identified a single QTL associated with the counteradaptation to Hamiltonella in L. fabarum on linkage group 2. Out of 120 genes located in this QTL, several genes encoding putative venoms may represent candidates for counteradaptation, as parasitoid wasps inject venoms into their hosts during oviposition

Generalized Ensemble and Tempering Simulations: A Unified View

From the underlying Master equations we derive one-dimensional stochastic processes that describe generalized ensemble simulations as well as tempering (simulated and parallel) simulations. The representations obtained are either in the form of a one-dimensional Fokker-Planck equation or a hopping process on a one-dimensional chain. In particular, we discuss the conditions under which these representations are valid approximate Markovian descriptions of the random walk in order parameter or control parameter space. They allow a unified discussion of the stationary distribution on, as well as of the stationary flow across each space. We demonstrate that optimizing the flow is equivalent to minimizing the first passage time for crossing the space, and discuss the consequences of our results for optimizing simulations. Finally, we point out the limitations of these representations under conditions of broken ergodicity.Comment: 11 pages Latex, 2 eps figures, revised version, typos corrected, PRE in pres

This elusive objective existence

Zurek's existential interpretation of quantum mechanics suffers from three classical prejudices, including the belief that space and time are intrinsically and infinitely differentiated. They compel him to relativize the concept of objective existence in two ways. The elimination of these prejudices makes it possible to recognize the quantum formalism's ontological implications - the relative and contingent reality of spatiotemporal distinctions and the extrinsic and finite spatiotemporal differentiation of the physical world - which in turn makes it possible to arrive at an unqualified objective existence. Contrary to a widespread misconception, viewing the quantum formalism as being fundamentally a probability algorithm does not imply that quantum mechanics is concerned with states of knowledge rather than states of Nature. On the contrary, it makes possible a complete and strongly objective description of the physical world that requires no reference to observers. What objectively exists, in a sense that requires no qualification, is the trajectories of macroscopic objects, whose fuzziness is empirically irrelevant, the properties and values of whose possession these trajectories provide indelible records, and the fuzzy and temporally undifferentiated states of affairs that obtain between measurements and are described by counterfactual probability assignments.Comment: To appear in IJQI; 21 pages, LaTe

Two-Photon Decays Reexamined: Cascade Contributions and Gauge Invariance

The purpose of this paper is to calculate the two-photon decay rate corresponding to the two-photon transitions nS->1S and nD->1S in hydrogenlike ions with a low nuclear charge number Z (for principal quantum numbers n = 2,...,8. Numerical results are obtained within a nonrelativistic framework, and the results are found to scale approximately as (Z alpha)^6/n^3, where alpha is the fine-structure constant. We also attempt to clarify a number of subtle issues regarding the treatment of the coherent, quasi-simultaneous emission of the two photons as opposed to one-photon cascades. In particular, the gauge invariance of the decay rate is shown explicitly.Comment: 10 pages, LaTe